Job ID = 2007104 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,907,389 reads read : 1,907,389 reads written : 1,907,389 spots read : 1,814,950 reads read : 1,814,950 reads written : 1,814,950 spots read : 1,781,263 reads read : 1,781,263 reads written : 1,781,263 spots read : 1,908,619 reads read : 1,908,619 reads written : 1,908,619 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529606.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529607.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529608.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR2529609.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:21 7412221 reads; of these: 7412221 (100.00%) were unpaired; of these: 366162 (4.94%) aligned 0 times 5954475 (80.33%) aligned exactly 1 time 1091584 (14.73%) aligned >1 times 95.06% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6972543 / 7046059 = 0.9896 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 15:55:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 15:55:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:55:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:55:33: #1 tag size is determined as 145 bps INFO @ Fri, 05 Jul 2019 15:55:33: #1 tag size = 145 INFO @ Fri, 05 Jul 2019 15:55:33: #1 total tags in treatment: 73516 INFO @ Fri, 05 Jul 2019 15:55:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:55:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:55:33: #1 tags after filtering in treatment: 73516 INFO @ Fri, 05 Jul 2019 15:55:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:55:33: #1 finished! INFO @ Fri, 05 Jul 2019 15:55:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:55:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:55:33: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 15:55:33: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 15:55:33: start model_add_line... INFO @ Fri, 05 Jul 2019 15:55:33: start X-correlation... INFO @ Fri, 05 Jul 2019 15:55:33: end of X-cor INFO @ Fri, 05 Jul 2019 15:55:33: #2 finished! INFO @ Fri, 05 Jul 2019 15:55:33: #2 predicted fragment length is 216 bps INFO @ Fri, 05 Jul 2019 15:55:33: #2 alternative fragment length(s) may be 28,55,79,104,123,152,167,194,216,241,261,293,300,328,351,379,406,439,456,489,513,534,560 bps INFO @ Fri, 05 Jul 2019 15:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.05_model.r WARNING @ Fri, 05 Jul 2019 15:55:33: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:55:33: #2 You may need to consider one of the other alternative d(s): 28,55,79,104,123,152,167,194,216,241,261,293,300,328,351,379,406,439,456,489,513,534,560 WARNING @ Fri, 05 Jul 2019 15:55:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:55:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:55:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 15:55:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:55:33: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 15:55:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.05_peaks.xls INFO @ Fri, 05 Jul 2019 15:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.05_summits.bed INFO @ Fri, 05 Jul 2019 15:55:34: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 2 millis BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 15:55:34: #1 tag size is determined as 145 bps INFO @ Fri, 05 Jul 2019 15:55:34: #1 tag size = 145 INFO @ Fri, 05 Jul 2019 15:55:34: #1 total tags in treatment: 73516 INFO @ Fri, 05 Jul 2019 15:55:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:55:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:55:34: #1 tags after filtering in treatment: 73516 INFO @ Fri, 05 Jul 2019 15:55:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:55:34: #1 finished! INFO @ Fri, 05 Jul 2019 15:55:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:55:34: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 15:55:34: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 15:55:34: start model_add_line... INFO @ Fri, 05 Jul 2019 15:55:34: start X-correlation... INFO @ Fri, 05 Jul 2019 15:55:34: end of X-cor INFO @ Fri, 05 Jul 2019 15:55:34: #2 finished! INFO @ Fri, 05 Jul 2019 15:55:34: #2 predicted fragment length is 216 bps INFO @ Fri, 05 Jul 2019 15:55:34: #2 alternative fragment length(s) may be 28,55,79,104,123,152,167,194,216,241,261,293,300,328,351,379,406,439,456,489,513,534,560 bps INFO @ Fri, 05 Jul 2019 15:55:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.10_model.r WARNING @ Fri, 05 Jul 2019 15:55:34: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:55:34: #2 You may need to consider one of the other alternative d(s): 28,55,79,104,123,152,167,194,216,241,261,293,300,328,351,379,406,439,456,489,513,534,560 WARNING @ Fri, 05 Jul 2019 15:55:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:55:34: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:55:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 15:55:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 15:55:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 15:55:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.10_peaks.xls INFO @ Fri, 05 Jul 2019 15:55:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:55:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.10_summits.bed INFO @ Fri, 05 Jul 2019 15:55:35: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 15:55:35: #1 tag size is determined as 145 bps INFO @ Fri, 05 Jul 2019 15:55:35: #1 tag size = 145 INFO @ Fri, 05 Jul 2019 15:55:35: #1 total tags in treatment: 73516 INFO @ Fri, 05 Jul 2019 15:55:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 15:55:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 15:55:35: #1 tags after filtering in treatment: 73516 INFO @ Fri, 05 Jul 2019 15:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 15:55:35: #1 finished! INFO @ Fri, 05 Jul 2019 15:55:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 15:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 15:55:35: #2 number of paired peaks: 325 WARNING @ Fri, 05 Jul 2019 15:55:35: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 05 Jul 2019 15:55:35: start model_add_line... INFO @ Fri, 05 Jul 2019 15:55:35: start X-correlation... INFO @ Fri, 05 Jul 2019 15:55:35: end of X-cor INFO @ Fri, 05 Jul 2019 15:55:35: #2 finished! INFO @ Fri, 05 Jul 2019 15:55:35: #2 predicted fragment length is 216 bps INFO @ Fri, 05 Jul 2019 15:55:35: #2 alternative fragment length(s) may be 28,55,79,104,123,152,167,194,216,241,261,293,300,328,351,379,406,439,456,489,513,534,560 bps INFO @ Fri, 05 Jul 2019 15:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.20_model.r WARNING @ Fri, 05 Jul 2019 15:55:35: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 15:55:35: #2 You may need to consider one of the other alternative d(s): 28,55,79,104,123,152,167,194,216,241,261,293,300,328,351,379,406,439,456,489,513,534,560 WARNING @ Fri, 05 Jul 2019 15:55:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 15:55:35: #3 Call peaks... INFO @ Fri, 05 Jul 2019 15:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 15:55:35: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 15:55:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.20_peaks.xls INFO @ Fri, 05 Jul 2019 15:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 15:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX2548191/ERX2548191.20_summits.bed INFO @ Fri, 05 Jul 2019 15:55:36: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling